In a recent article entitled On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE, Graur et al. dismantle ENCODEs evidence and conclusion that 80% of the human genome is functional. However, the article by Graur et al. contains assumptions and statements that are questionable. Primarily, the authors limit their evaluation of DNAs biological functions to informational roles, sidestepping putative non-informational functions. Here, I bring forward an old hypothesis on the evolution of genome size and on the role of so called junk DNA (jDNA), which might explain C-value enigma. According to this hypothesis, the jDNA functions as a defense mechanism against insertion mutagenesis by endogenous and exogenous inserting elements such as retroviruses, thereby protecting informational DNA sequences from inactivation or alteration of their expression. Notably, this model couples the mechanisms and the selective forces responsible for the origin of jDNA with its putative protective biological function, which represents a classic case of fighting fire with fire. One of the key tenets of this theory is that in humans and many other species, jDNAs serves as a protective mechanism against insertional oncogenic transformation. As an adaptive defense mechanism, the amount of protective DNA varies from one species to another based on the rate of its origin, insertional mutagenesis activity, and evolutionary constraints on genome size.

It's not a good idea to attack someone who; (a) is an expert in the field, (b) is intelligent and outspoken, and (c) has a blog. But that never stopped Claudiu Bandea before so why should it now?

The first problem with this hypothesis is that big eukaryotic genomes consist mostly of very few active transposable elements and numerous dead transposable elements. So, big genomes seem to need little protection. Moreover, a positive correlation exists between genome size and number of transposable elements. In 2002, Margaret Kidwell published a paper entitled “Transposable elements and the evolution of genome size in eukaryotes.” In it, she showed that an approximately linear relationship exists between total transposable element DNA and genome size. Copy numbers per family of transposable elements were found to be low and globally constrained in small genomes, but to vary widely in large genomes. Thus, the major characteristic of large genomes is the absence of selective constraint on transposable element copy number.

Given that the vast majority of transposable elements are dead, the most parsimonious explanation is that the continuous accumulation of dead transposable elements is the reason for genomes becoming large. Let me spell it out: the “large” part in “large genomes” is made of transposable elements. Genome do not become large first and then protect genetic information by becoming sinks of transposable elements.

The other problem with the protection-from-mutation hypothesis is that it assumes selection on mutation to be effective. Selection on mutation is referred to in population genetics as second-order selection. The reason is that this type of selection is anticipatory. It protects against a possibility, not an actuality. Second-order selection on mutation (mutability) requires huge effective population sizes, so huge in fact that they are only found in a few bacteria and viruses. Unfortunately for the protection-from-mutation hypothesis, genome size is known to be inversely correlated with effective population size. In other words, huge genomes are found in species that have very small effective population sizes. So small, in fact, that even regular selection (first-order selection) is not very effective.

Thomas Huxley was proven right again: "The great tragedy of Science is the slaying of a beautiful hypothesis by an ugly fact." Several ugly facts in this case.

I can't count the number of people who have tried to explain to Claudiu Bandea that his idea is ridiculous. Hopefully, this last embarrassment will silence him.

That may very well be true but the question is: Is there kind of some consistency in evolutionary theory regarding this assertion? Can I find more than one example that disproves this assumption and say; Well evolution must have taken some time off when this happened...? Anybody wanna bet? Dingene?

How would you respond or react to a post like this? Apparently, with silence!

Until now, the only exception was Quest, who could not restrain himself and exclaimed “OMG!!!”

Indeed, OMG!!! Unlike Larry Moran’s empty and arrogant take on my theory, a take that circumvented scientific arguments, in his post Dan Graur expressed his critique by presenting scientific evidence, which he thought go against my theory. On the rhetorical side of the story, Dan encouraged me to bring the theory forward so that other scientists can evaluate it, and he tweeted among other things: “Claudiu Bandea is a very thoughtful scientist. But on this occasion he is wrong”, which is reasonable. So, obviously, he did not consider my paper an “attack”, as portrayed by Larry.

For those interested in the scientific side of the story, here is an excerpt from my response to Dan’s arguments:

“As guardian-in-chief of junk DNA (jDNA), Dan Graur has been very sharp (to sharp, some people say) in his shattering critique of ENCODE’s conclusion that at least 80% of the human genome is functional. However, in his response above ("A Pre-Refuted Hypothesis on the Subject of "Junk DNA") to my paper he seems rather distracted.

To begin with, Dan refers to my hypothesis as a nucleotypic theory, which it is not. I would recommend he reads some of the many publications on the nucleotypic theory, such as those by Ryan Gregory (e.g. 1, 2); also, he might want to read my paper again, as I specifically addressed and questioned the nucleotypic theory; see also my recent PubMed Commons note (3) on Ford Doolittle’s article "Is junk DNA bunk? A critique of ENCODE" (4) in which I address the nucleotypic theory.

Next in his response, Dan expresses his love for my hypothesis, as he calls it "a beautiful hypothesis", only to realize (I presume under the pressure of his day-job as guardian of jDNA) that the ‘beaut’ was born "pre-refuted."

Then, Dan outlines a series of evidence/arguments that suppose to "pre-refute" the hypothesis but, surprisingly, are consistent with, or support the hypothesis:

(iv) "Copy numbers per family of transposable elements were found to be low and globally constrained in small genomes, but to vary widely in large genomes";

(v) "the major characteristic of large genomes is the absence of selective constraint on transposable element copy number";

(vi) "Given that the vast majority of transposable elements are dead, the most parsimonious explanation is that the continuous accumulation of dead transposable elements is the reason for genomes becoming large";

(vii) "Let me spell it out: the "large" part in "large genomes" is made of transposable elements";

(viii) "huge genomes are found in species that have very small effective population sizes", which, without a protective mechanism against insertion mutagenesis, would have little chance to survive evolutionarily.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.